* [[Overview]] to the system architecture at LCLS and real-time progress monitoring of data processing

* [[Overview]] to the system architecture at LCLS and real-time progress monitoring of data processing

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* Installation: ''cctbx.xfel'' is installed for general use at SLAC. To start using an existing installation, first [[Set up PSDM software | set up the PSDM software distribution]] and then [[Setup | set up ''cctbx.xfel'']].

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* Installation: there are two ways to get ''cctbx.xfel'':

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** ''cctbx.xfel'' is installed for general use at SLAC. To start using an existing installation, first [[Set up PSDM software | set up the PSDM software distribution]] and then [[Setup | set up ''cctbx.xfel'']].

Revision as of 10:43, 11 August 2015

Open-source tools for free-electron laser data processing

cctbx.xfel is a suite of software tools designed to process diffraction data from serial femtosecond crystallography (SFX) measurements at an X-ray free-electron laser (XFEL). Built on the Computational Crystallographic Toolbox (cctbx), the same toolbox on which PHENIX, LABELIT, and post-refinement and merging program, PRIME are built, it enables the user to solve difficult problems relating to processing XFEL data. The programs and modules provided by cctbx.xfel can reduce a large set of still diffraction images recorded at Stanford’s Linac Coherent Light Source (LCLS) to a single MTZ file containing merged reflection intensities suitable for structure solution.

cctbx.xfel resources

The tutorials on this wiki provide detailed instructions for indexing and integrating still diffraction images extracted from the raw data streams recorded at the LCLS, including pre-processing steps such as dark pedestal generation and refinement of the detector geometry of the Cornell–SLAC pixel array detectors (CSPAD) in use at the CXI and XPP end stations. The tutorials also cover tools to efficiently leverage the LCLS computing cluster to process the thousands to millions of diffraction images that can be recorded in a short time.

Overview to the system architecture at LCLS and real-time progress monitoring of data processing

2014 Workshop Tutorial: cctbx.xfel. Note, due to recent changes at LCLS, many of these tutorials are out of date for data collected late 2014 and onwards. For more up to date information, see above tutorials. For data collected before late 2014, these workshop tutorials are useful.